Error in Processing a Agilent converted mzXML file

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Jan 7, 2015, 9:48:14 PM1/7/15
It processed. but at the end, I got these errors:

Options {
  databases:   []
  v:           true
  h:           false
  i:           [mzMatch_output.peakml]
  annotations: [, relation.ship, codadw, charge]
  o:           mzMATCHoutput.txt
[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.
> # Processing finished!     Now extracting chromatogram images for each peak.
> chromdir <- "chromatograms"
> dir.create(chromdir)
> PeakMLData <- PeakML.Read("mzMatch_output.peakml",Rawpath=NULL)
Error: XML content does not seem to be XML: 'mzMatch_output.peakml'
Timing stopped at: 0 0.02 0.02
> peakIDlist <- c(1:length(unique(PeakMLData$peakDataMtx[,10])))
Error in unique(PeakMLData$peakDataMtx[, 10]) :
  error in evaluating the argument 'x' in selecting a method for function 'unique': Error: object 'PeakMLData' not found
> sampnames <- PeakMLData$sampleNames
Error: object 'PeakMLData' not found
> sampleslist<-c(1:max(PeakMLData$peakDataMtx[,9]))
Error: object 'PeakMLData' not found
> groupsets <- max(PeakMLData$peakDataMtx[,11])
Error: object 'PeakMLData' not found
> if (groupsets!=1) {samplegroups <- PeakMLData$phenoData} else {samplegroups <- sampnames}
Error: object 'groupsets' not found
> classnumbers <- samplegroups
Error: object 'samplegroups' not found
> for (i in 1:length(unique(samplegroups))){classnumbers <- sub(unique(classnumbers)[i], i, classnumbers)}
Error in unique(samplegroups) :
  error in evaluating the argument 'x' in selecting a method for function 'unique': Error: object 'samplegroups' not found
> for (a in 1:length(peakIDlist)){peakID <- peakIDlist[a]
+ hits <- which(PeakMLData$peakDataMtx[,10]==peakID)
+ intslist <- vector ("list")
+ rtlist <- vector ("list")
+ for (i in 1:length(hits)){intslist[[i]] <- PeakMLData$chromDataList[[hits[i]]][2,]
+ rtlist[[i]] <- (PeakMLData$chromDataList[[hits[i]]][3,]) / 60 }
+ maxint <- max(unlist(intslist))
+ minrt <-  min (unlist(rtlist))
+ maxrt <- max (unlist(rtlist))
+ samplenumbers <- PeakMLData$peakDataMtx[hits,9]
+ myfilename <- paste(getwd(),"/",chromdir,"/",peakID,".png",sep="")
+ png(myfilename, width = 350, height = 300)
+ lw = 0.2
+ par(fig=c(0,1-lw,0,1))
+ plot (1,1,xlab="RT (m)", ylab="Intensity", pch="", xlim=c(minrt,maxrt), ylim=c(0,maxint))
+ for (i in 1:length(hits)){if (PeakMLData$peakDataMtx[hits[i],9] %in% sampleslist==TRUE){
+ points (rtlist[[i]], intslist[[i]], type="l", col=classnumbers[samplenumbers [i]])}}
+ par(fig=c(0,1,0,1))
+ lpos <- par("usr")[2]-(lw /(1-lw ))*(par("usr")[2]-par("usr")[1])
+ legend (lpos, par("usr")[4], text.col=unique(classnumbers[sampleslist]), unique(samplegroups[sampleslist]), cex=0.8,xpd=TRUE)
Error: object 'peakIDlist' not found

Andris Jankevics

Jan 8, 2015, 6:17:52 AM1/8/15
to Li, Ideom
Hi Li,

Error message says that it can't locate file" mzMatch_output.peakml". Do you have this file in your output folder?

Best Regards,

Andris Jankevics

Research associate
Faculty of Life Sciences, Manchester Institute of Biotechnology, 
University of Manchester,
Manchester, United Kingdom

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Darren Creek

Jan 8, 2015, 6:54:00 PM1/8/15
to Andris Jankevics, Li, Ideom
Yes, my guess is the processing crashed either at the gap-filling or related peaks function. Try again from the step it failed at (it may have run out of memory but starting fresh may work - also double-check the RAM settings for these steps). 

Dr Darren Creek
NHMRC Career Development Fellow / Lecturer
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences
Monash University, Parkville campus
381 Royal Parade, Parkville, Vic, 3052

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